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angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
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Interactive files #1063

Open alex-l-kong opened 11 months ago

alex-l-kong commented 11 months ago

What is the purpose of this PR?

Closes #1029. Add interactive file selection to the notebooks.

How did you implement your changes

Use ipyfilechooser to allow users to interactively set home directories, such as base_dir, tiff_dir, etc.

Remaining issues

Start with notebooks 2 and 3. Gradually expand to include the others.

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alex-l-kong commented 10 months ago

RIP coverage, but otherwise it looks good. Did you plan on adding it to the other notebooks in this PR, or save it for later?

For now, I'm sandboxing all of these aesthetic improvements to Pixie. We can talk about more widespread adoption after we've fully fleshed them out.

camisowers commented 10 months ago

Just a minor comment on selecting a nested file which should have the same name for all users, so it probably can just be assigned by us rather than making them search for and choose it. I think if implemented throughout the other notebooks we should still maintain a lot of the subdir and file path setting automatically based on expected structure, and only use the path selection for top level dirs that might be different for people (i.e. base dir, image dir, segmentation dir).

alex-l-kong commented 10 months ago

Not a whole lot we can do about coverage, the original repo didn't have any test functions written for it. Don't think it's worth writing our own either.

alex-l-kong commented 10 months ago

@cliu72 just had to make one small tweak to ensure the function can retrieve the file names consistently on top of the full parent paths.